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Re: Problems with paedomorphic bird skull paper



Concerning the consensus, some quotations.

Like other methods that uses superimposition, Thin-Plate Splines (TPS) "uses" the consensus configuration for comparison and quantification of shape changes purposes:

"Consensus configuration - A single set of landmarks intended to represent the central tendency of an observed sample for the production of superimpositions, of a weight matrix, or some other morphometric purpose. Often a consensus configuration is computed to optimize some measure of fit to the full sample: in particular, the Procrustes mean shape is computed to minimize the sum of squared Procrustes distances from the the consensus landmarks to those of the sample." http://life.bio.sunysb.edu/morph/glossary/gloss1.html <http://life.bio.sunysb.edu/morph/glossary/gloss2.html>

"In the context of superimposition methods, this is the configuration to which data are fit. (...) The reference configuration corresponds to the point of tangency of the linear tangent space used to approximate Kendall's shape space. The mean configuration is usually used as the reference in order to minimize distortions caused by this approximation. When splines and warps are part of the analysis, the bending energy <http://life.bio.sunysb.edu/morph/glossary/gloss1.html#bending_energy> that goes with them is computed using the geometry of the grand mean shape, and the orthogonality that characterizes the partial warps is with respect to this particular formula for bending energy."
http://life.bio.sunysb.edu/morph/glossary/gloss2.html

Again, I've not deeply analyzed Mickey's post, just take a brief look at the images but, in my humble opinion, thought that my remarks could be valuable for this discussion.


Best,

Luis Azevedo Rodrigues

--
Luis Azevedo Rodrigues
Paleontologist (PhD)/Science communicator/Teacher
Publico Newspaper invited blog/Science Blogs Brazil
Ciencia Ao Natural - cienciaaonatural.net
twitter.com/CienAoNatural
independent.academia.edu/LuisARodrigues




On 23-07-2012 10:33, David Marjanovic wrote:
Rescued from truncation, comment below:

Hi Mickey,

I've just take a very brief look on your post "Does Confuciusornis
really have a skull configuration like juvenile Alligator? ".

Taking by granted that your Geometric Morphometrics (GM) knowledge is
average I just want to remember one thing on this group of morphometric
techniques:

1 -- the "wireframes" (Splines) indicate locations of deformation of an
individual compared to the consensus and not the original landmark
configuration.

Saying this I will read more carefully your post.

Best

Luis Azevedo Rodrigues

--
Luis Azevedo Rodrigues
Paleontologist (PhD)/Science communicator/Teacher
Publico Newspaper invited blog/Science Blogs Brazil
Ciencia Ao Natural - cienciaaonatural.net
twitter.com/CienAoNatural
independent.academia.edu/LuisARodrigues

What do you mean by "consensus"? An average of several individuals? That is obviously not the case here. For *Confuciusornis*, Bhullar et al. say they used specifically GMV-2132, _and_ no *C.* specimen looks _remotely_ like their wireframe. For the Montsec hatchling, there can't even be an average, because there is only a single specimen (LP-4450-IEI).

--
Luis Azevedo Rodrigues
Paleontologist (PhD)/Science communicator/Teacher
Publico Newspaper invited blog/Science Blogs Brazil
Ciencia Ao Natural - cienciaaonatural.net
twitter.com/CienAoNatural
independent.academia.edu/LuisARodrigues